Structure of the Anabaena PSI-monomer-IsiA supercomplex
Resolution: 2.62 Å
EM Method: Single-particle
Fitted PDBs: 7y3f
Q-score: 0.526
Nagao R, Kato K, Hamaguchi T, Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K, Shen JR
Nat Commun (2023) 14 pp. 920-920 [ Pubmed: 36805598 DOI: doi:10.1038/s41467-023-36504-1 ]
- Photosystem i reaction center subunit ix (5 kDa, Protein from Nostoc sp.)
- Iron stress-induced chlorophyll-binding protein (37 kDa, Protein from Nostoc sp.)
- Phylloquinone (450 Da, Ligand)
- Psam (4 kDa, Protein from Nostoc sp.)
- Photosystem i iron-sulfur center (8 kDa, Protein from Nostoc sp.)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Nostoc sp.)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Isia (27 kDa, Protein from Nostoc sp.)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit viii (5 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit xi (51 kDa, Protein from Nostoc sp.)
- Unknown (6 kDa, Protein from Nostoc sp.)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Nostoc sp.)
- Water (18 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 1 (83 kDa, Protein from Nostoc sp.)
- Psi-monomer-isia (640 kDa, Complex from Nostoc sp.)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i 4.8 kda protein (4 kDa, Protein from Nostoc sp.)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of a primordial cyanobacterial photosystem I
Resolution: 2.04 Å
EM Method: Single-particle
Fitted PDBs: 7f4v
Q-score: 0.752
Kato K, Hamaguchi T, Nagao R, Kawakami K, Ueno Y, Suzuki T, Uchida H, Murakami A, Nakajima Y, Yokono M, Akimoto S, Dohmae N, Yonekura K, Shen JR
bioRxiv (2022) [ DOI: doi:10.1101/2021.09.29.462462 ]
- Photosystem i reaction center subunit ii (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit xi (15 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i p700 chlorophyll a apoprotein a1 (86 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit xii (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Unknown protein (2 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit iv (7 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Psi trimer (1 MDa, Complex from Gloeobacter violaceus PCC 7421)
- Photosystem i p700 chlorophyll a apoprotein a2 (96 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit iii (19 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i iron-sulfur center (8 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Photosystem i reaction center subunit z (3 kDa, Protein from Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
- Menaquinone-4 (444 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
Structure of monomeric photosystem II
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 7eda
Q-score: 0.622
Yu H, Hamaguchi T, Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, Shen JR
Biochim Biophys Acta Bioenerg (2021) 1862 pp. 148471-148471 [ Pubmed: 34216574 DOI: doi:10.1016/j.bbabio.2021.148471 ]
- Unknown ligand (949 Da, Ligand)
- Photosystem ii (Complex from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein h (6 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein j (4 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Cytochrome c-550 (18 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Heme c (618 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit beta (5 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii 12 kda extrinsic protein (11 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- Pheophytin a (871 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Thermosynechococcus vulcanus)
- Fe (ii) ion (55 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
Cryo-EM Structure of PSII at 2.08 angstrom resolution
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 7d1u
Q-score: 0.757
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
- Beta-carotene (536 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii d2 protein (38 kDa, Protein from Thermosynechococcus vulcanus)
- Heme c (618 Da, Ligand)
- Photosystem ii cp43 reaction center protein (49 kDa, Protein from Thermosynechococcus vulcanus)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein z (6 kDa, Protein from Thermosynechococcus vulcanus)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome b559 subunit beta (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein k (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein l (4 kDa, Protein from Thermosynechococcus vulcanus)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Unknown ligand (Ligand)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (26 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein m (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein t (3 kDa, Protein from Thermosynechococcus vulcanus)
- Chloride ion (35 Da, Ligand)
- Photosystem ii protein d1 (37 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii 12 kda extrinsic protein (10 kDa, Protein from Thermosynechococcus vulcanus)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Thermosynechococcus vulcanus)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii reaction center protein x (4 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a (893 Da, Ligand)
- Cytochrome c-550 (15 kDa, Protein from Thermosynechococcus vulcanus)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein h (7 kDa, Protein from Thermosynechococcus vulcanus)
- Water (18 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem ii protein y (3 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM Structure of PSII at 2.22 angstrom resolution
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Cryo-EM Structure of PSII at 2.20 angstrom resolution
Kato K, Miyazaki N, Hamaguchi T, Nakajima Y, Akita F, Yonekura K, Shen JR
Commun Biol (2021) 4 pp. 382-382 [ Pubmed: 33753866 DOI: doi:10.1038/s42003-021-01919-3 ]
- Psii dimer (725 kDa, Complex from Thermosynechococcus vulcanus)
Structure of PSI-isiA supercomplex from Thermosynechococcus vulcanus
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 6k33
Q-score: 0.445
Akita F, Nagao R, Kato K, Nakajima Y, Yokono M, Ueno Y, Suzuki T, Dohmae N, Shen JR, Akimoto S, Miyazaki N
Commun Biol (2020) 3 pp. 232-232 [ Pubmed: 32393811 DOI: doi:10.1038/s42003-020-0949-6 ]
- Photosystem i iron-sulfur center (8 kDa, Protein from Thermosynechococcus vulcanus)
- Iron stress in-duced protein a (39 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Thermosynechococcus vulcanus)
- Phylloquinone (450 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Thermosynechococcus vulcanus)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem i reaction center subunit iv (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Thermosynechococcus vulcanus)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit psax (3 kDa, Protein from Thermosynechococcus vulcanus)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit psak (8 kDa, Protein from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Thermosynechococcus vulcanus)
- Psi-isia (1 MDa, Complex from Thermosynechococcus vulcanus)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Thermosynechococcus vulcanus)
- Iron/sulfur cluster (351 Da, Ligand)
Structure of PSI from H. hongdechloris grown under white light condition
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 6kmw
Q-score: 0.645
Kato K, Shinoda T, Nagao R, Akimoto S, Suzuki T, Dohmae N, Chen M, Allakhverdiev SI, Shen JR, Akita F, Miyazaki N, Tomo T
Nat Commun (2020) 11 pp. 238-238 [ DOI: doi:10.1038/s41467-019-13898-5 Pubmed: 31932639 ]
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Halomicronema hongdechloris C2206)
- White psi (Complex from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a1 (84 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Halomicronema hongdechloris C2206)
- Unknown ligand (Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit xi (16 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll a (893 Da, Ligand)
- Water (18 Da, Ligand)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Halomicronema hongdechloris C2206)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Halomicronema hongdechloris C2206)
Structure of PSI from H. hongdechloris grown under far-red light condition
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 6kmx
Q-score: 0.649
Kato K, Shinoda T, Nagao R, Akimoto S, Suzuki T, Dohmae N, Chen M, Allakhverdiev SI, Shen JR, Akita F, Miyazaki N, Tomo T
Nat Commun (2020) 11 pp. 238-238 [ DOI: doi:10.1038/s41467-019-13898-5 Pubmed: 31932639 ]
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll a isomer (893 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Halomicronema hongdechloris C2206)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit psak (9 kDa, Protein from Halomicronema hongdechloris C2206)
- Chlorophyll f (905 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (87 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i p700 chlorophyll a apoprotein a2 (83 kDa, Protein from Halomicronema hongdechloris C2206)
- Far-red psi (Complex from Halomicronema hongdechloris)
- Water (18 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosystem i reaction center subunit viii (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Unknown ligand (Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Halomicronema hongdechloris C2206)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Halomicronema hongdechloris C2206)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem i reaction center subunit xi (20 kDa, Protein from Halomicronema hongdechloris C2206)